Re: [gmx-users] Continuation of the gromacs job using gmx convert-tpr

[Own 12121325]

update:

I am trying using the way that you have suggested me

# the first step
gmx convert-tpr -s old.tpr -o new.tpr -extend 5
mdrun_mpi  -s new.tpr -deffnm old -cpi old -append

Here there is an issue:

Each time all pieces of the files will be merged into "old" (.trr .edr and
.cpt). But since I use always -deffnm old, the new check-point produced at
the end of the simulation will be always of the same name as the input
check-point (provided in the beginning)
so by the end of the each run I have to rename checkpoint file from old.cpt
to new.cpt and the next step should be

# the second step
gmx convert-tpr -s new.tpr -o new2.tpr -extend 5
mdrun_mpi  -s new2.tpr -deffnm old -cpi new -append
mv new.cpt new2.cpt

# the third step
gmx convert-tpr -s new2.tpr -o new3.tpr -extend 5
mdrun_mpi  -s new3.tpr -deffnm old -cpi new2 -append
mv new2.cpt new3.cpt

etc.

So the trajectory and edr files will be always the same but check-point
files updated (if I will be needed to go back )


Actually it may produce some mismatching between the files...



2018-06-22 16:22 GMT+02:00 Own 12121325 :

> Thanks Mark!
>
>
> assuming that I am interesting to obtain separate files for the each step
> I need just one command:
>
> mdrun -v -deffnm step7_1 -cpi step7_1.cpt -noappend
> that each time should create step7_1part002 etc
>
> but in case if I want to set manes of each pieces manually (it sounds
> crazy but in fact I need to do follow this way!) does the method with gmx
> convert-tpr in principle produce separate pieces correctly?
>
> gmx convert-tpr -s step7_1.tpr -o step7_2.tpr -extend 5
> mdrun -v -deffnm step7_2 -cpi step7_1.cpt
>
> in earlier versions I did in the same way but without cpt file and it
> worked good:
>
> gmx convert-tpr -s step7_1.tpr -trr step7_1 -edr step7_1 -o step7_2.tpr
> -extend 5
> mdrun -v -deffnm step7_2
>
>
>
> 2018-06-22 15:02 GMT+02:00 Mark Abraham :
>
>> Hi,
>>
>> There are some differences in recent GROMACS versions here (because the
>> old
>> implementations were not robust enough), but the checkpoint restart will
>> not work with appending unless it finds the output files named in the .cpt
>> match those on the command line (here, from -deffnm). You're making extra
>> work for yourself in several ways.
>>
>> I encourage you to not use -deffnm with a new name that merely signifies
>> that the extension happened. There's no physical and no real
>> organizational
>> reason to do this.
>>
>> If you want numbered output files for each step, then start your
>> simulations with -noappend and let mdrun number them automatically. But
>> IMO
>> all that does is make work for you later, concatenating the files again.
>>
>> If you want appending to work after extending to the number of steps, use
>> -s new.tpr -deffnm old rather than -deffnm new, because the former doesn't
>> create name mismatches between those output files that the checkpoint
>> remembers and those you've instructed mdrun to use now.
>>
>> And if your reason for using -deffnm is that you want to have multiple
>> simulation steps in the same directory, bear in mind that using a single
>> directory to contain a single step is much more robust (you are using the
>> standard way of grouping related files, called a directory, and using cd
>> is
>> not any more difficult than -deffnm), and you can just use the default
>> file
>> naming:
>>
>> (cd step7; mpirun -np whatever gmx_mpi mdrun -s extended)
>>
>> Mark
>>
>> On Fri, Jun 22, 2018 at 11:07 AM Own 12121325 
>> wrote:
>>
>> > thanks Mark!
>> >
>> > could you please also confirm that my method of the prolongation of the
>> > simulation would be correct
>> >
>> > #entend simulation for 50 ns and save these pieces as the separate files
>> > with the name step7_2*
>> > gmx convert-tpr -s step7_1.tpr -o step7_2.tpr -extend 5
>> > mdrun -v -deffnm step7_2 -cpi step7_1.cpt
>> >
>> > 2018-06-22 10:57 GMT+02:00 Mark Abraham :
>> >
>> > > Hi,
>> > >
>> > > The previous checkpoint has the _prev suffix, in case there is a
>> problem
>> > > that might require you to go further back in time.
>> > >
>> > > Mark
>> > >
>> > > On Fri, Jun 22, 2018, 10:46 Own 12121325 
>> wrote:
>> > >
>> > > > P.S. what the difference between name.cpt and name_prev.cpt
>> produced by
>> > > > mdrun? What check-point should correspond to the last snapshot in
>> trr
>> > > file
>> &

Re: [gmx-users] Continuation of the gromacs job using gmx convert-tpr

[Own 12121325]

Thanks Mark!


assuming that I am interesting to obtain separate files for the each step I
need just one command:

mdrun -v -deffnm step7_1 -cpi step7_1.cpt -noappend
that each time should create step7_1part002 etc

but in case if I want to set manes of each pieces manually (it sounds crazy
but in fact I need to do follow this way!) does the method with gmx
convert-tpr in principle produce separate pieces correctly?

gmx convert-tpr -s step7_1.tpr -o step7_2.tpr -extend 5
mdrun -v -deffnm step7_2 -cpi step7_1.cpt

in earlier versions I did in the same way but without cpt file and it
worked good:

gmx convert-tpr -s step7_1.tpr -trr step7_1 -edr step7_1 -o step7_2.tpr
-extend 5
mdrun -v -deffnm step7_2



2018-06-22 15:02 GMT+02:00 Mark Abraham :

> Hi,
>
> There are some differences in recent GROMACS versions here (because the old
> implementations were not robust enough), but the checkpoint restart will
> not work with appending unless it finds the output files named in the .cpt
> match those on the command line (here, from -deffnm). You're making extra
> work for yourself in several ways.
>
> I encourage you to not use -deffnm with a new name that merely signifies
> that the extension happened. There's no physical and no real organizational
> reason to do this.
>
> If you want numbered output files for each step, then start your
> simulations with -noappend and let mdrun number them automatically. But IMO
> all that does is make work for you later, concatenating the files again.
>
> If you want appending to work after extending to the number of steps, use
> -s new.tpr -deffnm old rather than -deffnm new, because the former doesn't
> create name mismatches between those output files that the checkpoint
> remembers and those you've instructed mdrun to use now.
>
> And if your reason for using -deffnm is that you want to have multiple
> simulation steps in the same directory, bear in mind that using a single
> directory to contain a single step is much more robust (you are using the
> standard way of grouping related files, called a directory, and using cd is
> not any more difficult than -deffnm), and you can just use the default file
> naming:
>
> (cd step7; mpirun -np whatever gmx_mpi mdrun -s extended)
>
> Mark
>
> On Fri, Jun 22, 2018 at 11:07 AM Own 12121325 
> wrote:
>
> > thanks Mark!
> >
> > could you please also confirm that my method of the prolongation of the
> > simulation would be correct
> >
> > #entend simulation for 50 ns and save these pieces as the separate files
> > with the name step7_2*
> > gmx convert-tpr -s step7_1.tpr -o step7_2.tpr -extend 5
> > mdrun -v -deffnm step7_2 -cpi step7_1.cpt
> >
> > 2018-06-22 10:57 GMT+02:00 Mark Abraham :
> >
> > > Hi,
> > >
> > > The previous checkpoint has the _prev suffix, in case there is a
> problem
> > > that might require you to go further back in time.
> > >
> > > Mark
> > >
> > > On Fri, Jun 22, 2018, 10:46 Own 12121325 
> wrote:
> > >
> > > > P.S. what the difference between name.cpt and name_prev.cpt produced
> by
> > > > mdrun? What check-point should correspond to the last snapshot in trr
> > > file
> > > > ?
> > > >
> > > > 2018-06-22 10:17 GMT+02:00 Own 12121325 :
> > > >
> > > > > In fact there is an alternative trick :-)
> > > > > If I rename a tpr file via gmx convert-tpr  and then run mdrun
> using
> > > this
> > > > > new tpr as well as previous checkpoint, it will produce all pieces
> of
> > > the
> > > > > trajectory in the separate file:
> > > > >
> > > > > gmx convert-tpr -s step7_1.tpr -o step7_2.tpr -extend 5
> > > > > mpirun -np ${NB_TASKS} mdrun -v -deffnm step7_2 -cpi step7_1.cpt
> > > > >
> > > > > If I add -noappend flag to the mdrun, its also do the same job but
> > also
> > > > > will add suffix pat002 to each of the new file (that is not
> necessary
> > > for
> > > > > me since I have already renamed tpr).
> > > > >
> > > > > Gleb
> > > > >
> > > > >
> > > > > 2018-06-21 14:17 GMT+02:00 Justin Lemkul :
> > > > >
> > > > >>
> > > > >>
> > > > >> On 6/21/18 2:35 AM, Own 12121325 wrote:
> > > > >>
> > > > >>> and without append flag it will produce an output in the separate
> > > file,
> > > > >>> won't it?
> > > > &g

Re: [gmx-users] Continuation of the gromacs job using gmx convert-tpr

[Own 12121325]

thanks Mark!

could you please also confirm that my method of the prolongation of the
simulation would be correct

#entend simulation for 50 ns and save these pieces as the separate files
with the name step7_2*
gmx convert-tpr -s step7_1.tpr -o step7_2.tpr -extend 5
mdrun -v -deffnm step7_2 -cpi step7_1.cpt

2018-06-22 10:57 GMT+02:00 Mark Abraham :

> Hi,
>
> The previous checkpoint has the _prev suffix, in case there is a problem
> that might require you to go further back in time.
>
> Mark
>
> On Fri, Jun 22, 2018, 10:46 Own 12121325  wrote:
>
> > P.S. what the difference between name.cpt and name_prev.cpt produced by
> > mdrun? What check-point should correspond to the last snapshot in trr
> file
> > ?
> >
> > 2018-06-22 10:17 GMT+02:00 Own 12121325 :
> >
> > > In fact there is an alternative trick :-)
> > > If I rename a tpr file via gmx convert-tpr  and then run mdrun using
> this
> > > new tpr as well as previous checkpoint, it will produce all pieces of
> the
> > > trajectory in the separate file:
> > >
> > > gmx convert-tpr -s step7_1.tpr -o step7_2.tpr -extend 5
> > > mpirun -np ${NB_TASKS} mdrun -v -deffnm step7_2 -cpi step7_1.cpt
> > >
> > > If I add -noappend flag to the mdrun, its also do the same job but also
> > > will add suffix pat002 to each of the new file (that is not necessary
> for
> > > me since I have already renamed tpr).
> > >
> > > Gleb
> > >
> > >
> > > 2018-06-21 14:17 GMT+02:00 Justin Lemkul :
> > >
> > >>
> > >>
> > >> On 6/21/18 2:35 AM, Own 12121325 wrote:
> > >>
> > >>> and without append flag it will produce an output in the separate
> file,
> > >>> won't it?
> > >>>
> > >>
> > >> No, because appending is the default behavior. Specifying -append just
> > >> invokes what mdrun does on its own. If you want a separate file, add
> > >> -noappend to your mdrun command.
> > >>
> > >> -Justin
> > >>
> > >>
> > >> gmx convert-tpr -s init.tpr -o next.tpr -extend 50
> > >>> gmx mdrun -s next.tpr -cpi the_last_chekpoint.cpt
> > >>>
> > >>> 2018-06-21 1:12 GMT+02:00 Justin Lemkul :
> > >>>
> > >>>
> > >>>> On 6/19/18 4:45 AM, Own 12121325 wrote:
> > >>>>
> > >>>> Hello Justin,
> > >>>>>
> > >>>>> could you specify please a bit more. Following your method, if the
> > >>>>> simulation has been terminated by crash without producing gro file
> so
> > >>>>> to
> > >>>>> re-initiate it I only need one command:
> > >>>>>
> > >>>>> gmx mdrun -s initial.tpr -cpi the_last_chekpoint.cpt -append
> > >>>>>
> > >>>>> where the last_checkpoint should be something like initial.cpt or
> > >>>>> initial_prev.cpt
> > >>>>>
> > >>>>> Right.
> > >>>>
> > >>>> but In case if my simulation has been finished correctly e.g. for 50
> > ns
> > >>>> and
> > >>>>
> > >>>>> I now need to extend it for another 50 ns,  should I do the
> following
> > >>>>> trick
> > >>>>> with 2 GMX programs:
> > >>>>>
> > >>>>> gmx convert-tpr -s init.tpr -o next.tpr -extend 50
> > >>>>> gmx mdrun -s next.tpr -cpi the_last_chekpoint.cpt -append
> > >>>>>
> > >>>>> it will produce the second part of the trajectory as the new file
> > >>>>> (next.trr) or merge together the first and the second part ?
> > >>>>>
> > >>>>> You're specifying -append, so the output will be concatenated by
> > mdrun.
> > >>>> That's also been default behavior for as long as I can remember, too
> > :)
> > >>>>
> > >>>> -Justin
> > >>>>
> > >>>> --
> > >>>> ==
> > >>>>
> > >>>> Justin A. Lemkul, Ph.D.
> > >>>> Assistant Professor
> > >>>> Virginia Tech Department of Biochemistry
> > >>>>
> > >>>> 303 Engel Hall
> > >>>> 340 West Campus D

Re: [gmx-users] Continuation of the gromacs job using gmx convert-tpr

[Own 12121325]

P.S. what the difference between name.cpt and name_prev.cpt produced by
mdrun? What check-point should correspond to the last snapshot in trr file ?

2018-06-22 10:17 GMT+02:00 Own 12121325 :

> In fact there is an alternative trick :-)
> If I rename a tpr file via gmx convert-tpr  and then run mdrun using this
> new tpr as well as previous checkpoint, it will produce all pieces of the
> trajectory in the separate file:
>
> gmx convert-tpr -s step7_1.tpr -o step7_2.tpr -extend 5
> mpirun -np ${NB_TASKS} mdrun -v -deffnm step7_2 -cpi step7_1.cpt
>
> If I add -noappend flag to the mdrun, its also do the same job but also
> will add suffix pat002 to each of the new file (that is not necessary for
> me since I have already renamed tpr).
>
> Gleb
>
>
> 2018-06-21 14:17 GMT+02:00 Justin Lemkul :
>
>>
>>
>> On 6/21/18 2:35 AM, Own 12121325 wrote:
>>
>>> and without append flag it will produce an output in the separate file,
>>> won't it?
>>>
>>
>> No, because appending is the default behavior. Specifying -append just
>> invokes what mdrun does on its own. If you want a separate file, add
>> -noappend to your mdrun command.
>>
>> -Justin
>>
>>
>> gmx convert-tpr -s init.tpr -o next.tpr -extend 50
>>> gmx mdrun -s next.tpr -cpi the_last_chekpoint.cpt
>>>
>>> 2018-06-21 1:12 GMT+02:00 Justin Lemkul :
>>>
>>>
>>>> On 6/19/18 4:45 AM, Own 12121325 wrote:
>>>>
>>>> Hello Justin,
>>>>>
>>>>> could you specify please a bit more. Following your method, if the
>>>>> simulation has been terminated by crash without producing gro file so
>>>>> to
>>>>> re-initiate it I only need one command:
>>>>>
>>>>> gmx mdrun -s initial.tpr -cpi the_last_chekpoint.cpt -append
>>>>>
>>>>> where the last_checkpoint should be something like initial.cpt or
>>>>> initial_prev.cpt
>>>>>
>>>>> Right.
>>>>
>>>> but In case if my simulation has been finished correctly e.g. for 50 ns
>>>> and
>>>>
>>>>> I now need to extend it for another 50 ns,  should I do the following
>>>>> trick
>>>>> with 2 GMX programs:
>>>>>
>>>>> gmx convert-tpr -s init.tpr -o next.tpr -extend 50
>>>>> gmx mdrun -s next.tpr -cpi the_last_chekpoint.cpt -append
>>>>>
>>>>> it will produce the second part of the trajectory as the new file
>>>>> (next.trr) or merge together the first and the second part ?
>>>>>
>>>>> You're specifying -append, so the output will be concatenated by mdrun.
>>>> That's also been default behavior for as long as I can remember, too :)
>>>>
>>>> -Justin
>>>>
>>>> --
>>>> ==
>>>>
>>>> Justin A. Lemkul, Ph.D.
>>>> Assistant Professor
>>>> Virginia Tech Department of Biochemistry
>>>>
>>>> 303 Engel Hall
>>>> 340 West Campus Dr.
>>>> Blacksburg, VA 24061
>>>>
>>>> jalem...@vt.edu | (540) 231-3129
>>>> http://www.thelemkullab.com
>>>>
>>>> ==
>>>>
>>>> --
>>>> Gromacs Users mailing list
>>>>
>>>> * Please search the archive at http://www.gromacs.org/Support
>>>> /Mailing_Lists/GMX-Users_List before posting!
>>>>
>>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>>>
>>>> * For (un)subscribe requests visit
>>>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>>>> send a mail to gmx-users-requ...@gromacs.org.
>>>>
>>>>
>> --
>> ==
>>
>> Justin A. Lemkul, Ph.D.
>> Assistant Professor
>> Virginia Tech Department of Biochemistry
>>
>> 303 Engel Hall
>> 340 West Campus Dr.
>> Blacksburg, VA 24061
>>
>> jalem...@vt.edu | (540) 231-3129
>> http://www.thelemkullab.com
>>
>> ==
>>
>> --
>> Gromacs Users mailing list
>>
>> * Please search the archive at http://www.gromacs.org/Support
>> /Mailing_Lists/GMX-Users_List before posting!
>>
>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>
>> * For (un)subscribe requests visit
>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>> send a mail to gmx-users-requ...@gromacs.org.
>>
>
>
-- 
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Re: [gmx-users] Continuation of the gromacs job using gmx convert-tpr

[Own 12121325]

In fact there is an alternative trick :-)
If I rename a tpr file via gmx convert-tpr  and then run mdrun using this
new tpr as well as previous checkpoint, it will produce all pieces of the
trajectory in the separate file:

gmx convert-tpr -s step7_1.tpr -o step7_2.tpr -extend 5
mpirun -np ${NB_TASKS} mdrun -v -deffnm step7_2 -cpi step7_1.cpt

If I add -noappend flag to the mdrun, its also do the same job but also
will add suffix pat002 to each of the new file (that is not necessary for
me since I have already renamed tpr).

Gleb


2018-06-21 14:17 GMT+02:00 Justin Lemkul :

>
>
> On 6/21/18 2:35 AM, Own 12121325 wrote:
>
>> and without append flag it will produce an output in the separate file,
>> won't it?
>>
>
> No, because appending is the default behavior. Specifying -append just
> invokes what mdrun does on its own. If you want a separate file, add
> -noappend to your mdrun command.
>
> -Justin
>
>
> gmx convert-tpr -s init.tpr -o next.tpr -extend 50
>> gmx mdrun -s next.tpr -cpi the_last_chekpoint.cpt
>>
>> 2018-06-21 1:12 GMT+02:00 Justin Lemkul :
>>
>>
>>> On 6/19/18 4:45 AM, Own 12121325 wrote:
>>>
>>> Hello Justin,
>>>>
>>>> could you specify please a bit more. Following your method, if the
>>>> simulation has been terminated by crash without producing gro file so to
>>>> re-initiate it I only need one command:
>>>>
>>>> gmx mdrun -s initial.tpr -cpi the_last_chekpoint.cpt -append
>>>>
>>>> where the last_checkpoint should be something like initial.cpt or
>>>> initial_prev.cpt
>>>>
>>>> Right.
>>>
>>> but In case if my simulation has been finished correctly e.g. for 50 ns
>>> and
>>>
>>>> I now need to extend it for another 50 ns,  should I do the following
>>>> trick
>>>> with 2 GMX programs:
>>>>
>>>> gmx convert-tpr -s init.tpr -o next.tpr -extend 50
>>>> gmx mdrun -s next.tpr -cpi the_last_chekpoint.cpt -append
>>>>
>>>> it will produce the second part of the trajectory as the new file
>>>> (next.trr) or merge together the first and the second part ?
>>>>
>>>> You're specifying -append, so the output will be concatenated by mdrun.
>>> That's also been default behavior for as long as I can remember, too :)
>>>
>>> -Justin
>>>
>>> --
>>> ==
>>>
>>> Justin A. Lemkul, Ph.D.
>>> Assistant Professor
>>> Virginia Tech Department of Biochemistry
>>>
>>> 303 Engel Hall
>>> 340 West Campus Dr.
>>> Blacksburg, VA 24061
>>>
>>> jalem...@vt.edu | (540) 231-3129
>>> http://www.thelemkullab.com
>>>
>>> ==
>>>
>>> --
>>> Gromacs Users mailing list
>>>
>>> * Please search the archive at http://www.gromacs.org/Support
>>> /Mailing_Lists/GMX-Users_List before posting!
>>>
>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>>
>>> * For (un)subscribe requests visit
>>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>>> send a mail to gmx-users-requ...@gromacs.org.
>>>
>>>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Virginia Tech Department of Biochemistry
>
> 303 Engel Hall
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalem...@vt.edu | (540) 231-3129
> http://www.thelemkullab.com
>
> ==
>
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/Support
> /Mailing_Lists/GMX-Users_List before posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-requ...@gromacs.org.
>
-- 
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Re: [gmx-users] Continuation of the gromacs job using gmx convert-tpr

[Own 12121325]

and without append flag it will produce an output in the separate file,
won't it?

gmx convert-tpr -s init.tpr -o next.tpr -extend 50
gmx mdrun -s next.tpr -cpi the_last_chekpoint.cpt

2018-06-21 1:12 GMT+02:00 Justin Lemkul :

>
>
> On 6/19/18 4:45 AM, Own 12121325 wrote:
>
>> Hello Justin,
>>
>> could you specify please a bit more. Following your method, if the
>> simulation has been terminated by crash without producing gro file so to
>> re-initiate it I only need one command:
>>
>> gmx mdrun -s initial.tpr -cpi the_last_chekpoint.cpt -append
>>
>> where the last_checkpoint should be something like initial.cpt or
>> initial_prev.cpt
>>
>
> Right.
>
> but In case if my simulation has been finished correctly e.g. for 50 ns and
>> I now need to extend it for another 50 ns,  should I do the following
>> trick
>> with 2 GMX programs:
>>
>> gmx convert-tpr -s init.tpr -o next.tpr -extend 50
>> gmx mdrun -s next.tpr -cpi the_last_chekpoint.cpt -append
>>
>> it will produce the second part of the trajectory as the new file
>> (next.trr) or merge together the first and the second part ?
>>
>
> You're specifying -append, so the output will be concatenated by mdrun.
> That's also been default behavior for as long as I can remember, too :)
>
> -Justin
>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Virginia Tech Department of Biochemistry
>
> 303 Engel Hall
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalem...@vt.edu | (540) 231-3129
> http://www.thelemkullab.com
>
> ==
>
> --
> Gromacs Users mailing list
>
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Re: [gmx-users] Continuation of the gromacs job using gmx convert-tpr

[Own 12121325]

Hello Justin,

could you specify please a bit more. Following your method, if the
simulation has been terminated by crash without producing gro file so to
re-initiate it I only need one command:

gmx mdrun -s initial.tpr -cpi the_last_chekpoint.cpt -append

where the last_checkpoint should be something like initial.cpt or
initial_prev.cpt

but In case if my simulation has been finished correctly e.g. for 50 ns and
I now need to extend it for another 50 ns,  should I do the following trick
with 2 GMX programs:

gmx convert-tpr -s init.tpr -o next.tpr -extend 50
gmx mdrun -s next.tpr -cpi the_last_chekpoint.cpt -append

it will produce the second part of the trajectory as the new file
(next.trr) or merge together the first and the second part ?

Thank you!

Gleb


2018-06-18 21:00 GMT+02:00 Justin Lemkul :

>
>
> On 6/18/18 9:11 AM, Own 12121325 wrote:
>
>> thanks Justin for the suggestions!
>>
>> but generally this antiquated approach produces correct thermodynamical
>> ensembles (since I do not call grompp again), doesn't it?  Following this
>> method the last snapshot from the trajectory will be taken to continue
>> job,
>> right ?
>>
>
> Possibly. I haven't done this since the 3.3.x series, though, because
> checkpoints guarantee an exact continuation. The combination of .trr + .edr
> is not exact but is close. It probably all comes out in the noise of the
> simulation, but if you can choose between an exact continuation and an
> approximate one, why not be exact? :)
>
> -Justin
>
>
> 2018-06-15 14:22 GMT+02:00 Justin Lemkul :
>>
>>
>>> On 6/14/18 4:01 AM, Own 12121325 wrote:
>>>
>>> Hello,
>>>>
>>>> I wonder to know if it's necessary to provide edr file for the completed
>>>> part of the simulation in order to continue the md job assuming that I
>>>> provide the trajectory (with coordinates and velocities) using
>>>> gmx convert-tpr.
>>>>
>>>> Does the ensembles produced by mdrun will be the same following these
>>>> two
>>>> methods of the continuation:
>>>>
>>>> gmx convert-tpr -s prev.tpr -f prev.trr -o next.tpr -extend 1000
>>>> gmx mdrun -v -deffnm next
>>>>
>>>> compared to
>>>>
>>>> gmx convert-tpr -s prev.tpr -f prev.trr *-e prev.edr* -o next.tpr
>>>> -extend
>>>> 1000
>>>> gmx mdrun -v -deffnm next
>>>>
>>>> You don't use either .trr or .edr files. Just generate the new .tpr file
>>> with however much more time you want and pick up from the exact time
>>> point
>>> you were with mdrun -cpi prev.cpt. Use of .trr and .edr files to extend
>>> simulations is an antiquated approach.
>>>
>>> -Justin
>>>
>>> --
>>> ==
>>>
>>> Justin A. Lemkul, Ph.D.
>>> Assistant Professor
>>> Virginia Tech Department of Biochemistry
>>>
>>> 303 Engel Hall
>>> 340 West Campus Dr.
>>> Blacksburg, VA 24061
>>>
>>> jalem...@vt.edu | (540) 231-3129
>>> http://www.thelemkullab.com
>>>
>>> ==
>>>
>>> --
>>> Gromacs Users mailing list
>>>
>>> * Please search the archive at http://www.gromacs.org/Support
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>>> send a mail to gmx-users-requ...@gromacs.org.
>>>
>>>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Virginia Tech Department of Biochemistry
>
> 303 Engel Hall
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalem...@vt.edu | (540) 231-3129
> http://www.thelemkullab.com
>
> ==
>
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Re: [gmx-users] Continuation of the gromacs job using gmx convert-tpr

[Own 12121325]

thanks Justin for the suggestions!

but generally this antiquated approach produces correct thermodynamical
ensembles (since I do not call grompp again), doesn't it?  Following this
method the last snapshot from the trajectory will be taken to continue job,
right ?

2018-06-15 14:22 GMT+02:00 Justin Lemkul :

>
>
> On 6/14/18 4:01 AM, Own 12121325 wrote:
>
>> Hello,
>>
>> I wonder to know if it's necessary to provide edr file for the completed
>> part of the simulation in order to continue the md job assuming that I
>> provide the trajectory (with coordinates and velocities) using
>> gmx convert-tpr.
>>
>> Does the ensembles produced by mdrun will be the same following these two
>> methods of the continuation:
>>
>> gmx convert-tpr -s prev.tpr -f prev.trr -o next.tpr -extend 1000
>> gmx mdrun -v -deffnm next
>>
>> compared to
>>
>> gmx convert-tpr -s prev.tpr -f prev.trr *-e prev.edr* -o next.tpr -extend
>> 1000
>> gmx mdrun -v -deffnm next
>>
>
> You don't use either .trr or .edr files. Just generate the new .tpr file
> with however much more time you want and pick up from the exact time point
> you were with mdrun -cpi prev.cpt. Use of .trr and .edr files to extend
> simulations is an antiquated approach.
>
> -Justin
>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Virginia Tech Department of Biochemistry
>
> 303 Engel Hall
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalem...@vt.edu | (540) 231-3129
> http://www.thelemkullab.com
>
> ==
>
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/Support
> /Mailing_Lists/GMX-Users_List before posting!
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[gmx-users] Continuation of the gromacs job using gmx convert-tpr

[Own 12121325]

Hello,

I wonder to know if it's necessary to provide edr file for the completed
part of the simulation in order to continue the md job assuming that I
provide the trajectory (with coordinates and velocities) using
gmx convert-tpr.

Does the ensembles produced by mdrun will be the same following these two
methods of the continuation:

gmx convert-tpr -s prev.tpr -f prev.trr -o next.tpr -extend 1000
gmx mdrun -v -deffnm next

compared to

gmx convert-tpr -s prev.tpr -f prev.trr *-e prev.edr* -o next.tpr -extend
1000
gmx mdrun -v -deffnm next

Thanks you in advance!
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[gmx-users] Surface tension calculations via gmx energy?

[Own 12121325]

Dear GROMACS users,

Using gmx energy I am trying to compute surface tension for the membrane
system in GROMACS under different surface tension. In the model surface
tension was modeled by various negative lateral pressure:

Pxy surf*surftension

1 bar -33.8847
-10 bar 155.696
-20 bar 240.326
-30 bar 277.994
-40 bar 367.037

Now I need to extract from these values a value for surface tension in
dyn/cm (1 bar*nm = 0.1 mN/m = 0.1 dyn/cm).

Question: what is the number of surfaces [surf*] should be for membrane
system?

Thanks in advance
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[gmx-users] Surface tension from gmx energy

[Own 12121325]

Dear Gromacs Users!

I am interesting how is possible to obtain the value for the surface
tension via the output from the gmx energy.

E.g. on the example I have two outputs where in the second case the ST were
introduced via the adding the negative lateral pressure along XY:


# 1)  no surface tension; 1 bar in XY
Energy  Average   Err.Est.   RMSD  Tot-Drift
---
#Surf*SurfTen   5.732714.2 
  3314.05
-19.0927   (bar nm)


# 2) -10 bar in xy

Energy  Average   Err.Est.   RMSD  Tot-Drift
---
#Surf*SurfTen   106.5236.1 
   3072.3
-23.3618   (bar nm)

How to convert these values of the averages to the dyn/cm ?

Thanks you!

Gleb
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[gmx-users] On the choosing of tau_t for SD integrator

[Own 12121325]

Dear Gromacs Users,

I have found that 2 ps is a standard value for the tau_t for SD integrator.
Since it is a reverse friction constant, does it means that the values
below 2 ps will provide stronger coupling with thermostat (more virtual
collisions => more viscosity) and the values above 2 ps should reduce
viscosity.

I am interesting how the changing of tau_t will modify the behavior of
solvent in the simulations with Langevin's dynamics e.g in case of the
simulation of the flow?

Thanks so much for help!
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Re: [gmx-users] Simulation in NPgT ensemble

[Own 12121325]

a question - If I add a negative pressure in xy for the membrane
stretching, using an approach:

pcoupltype = semiisotropic
tau_p 1 1
compressibility 4.5e-5 4.5e-5
ref_p -100 1

will it also increase the diffusion of the solvent along the xy plane of
the membrane, thus mimicking effect of the flow?
Or for that case I need to switch to full anisotropic pressure coupling,
introducing a negative pressure along one selected direction ( e.g along x
or y)?

thanks!

2017-09-26 12:37 GMT+02:00 Own 12121325 <own12121...@gmail.com>:

> So the question - what the difference will be between A and B and what
> method is better for the lipid bilayer?
>
> (A)
> pcoupltype = semiisotropic
> tau_p 1 1
> compressibility 4.5e-5 4.5e-5
> ref_p -100 1
>
> if the system size in the z-direction is ~ 10nm, then
> this should give a surface tension of (Pz-Plat)*Lz ==
> (1+100)bar*10 nm ~ 10^3 bar nm = 10^3*10^5 N/m2 *10^-9
> m
> =100mN/m assuming the z-dimension Lz remains
> approximately 10 nm throughout the window of
> calculation.
>
>
> (B)
> pcoupltype = surface-tension
> tau_p 1 1
> compressibility 4.5e-5 0 ; Z is fixed
> ref_p -1000 1 ; -1000 is actual surface tension which is the compression
> for the membrane along xy.
>
> 2017-09-25 17:29 GMT+02:00 Own 12121325 <own12121...@gmail.com>:
>
>> Thanks, Andre!
>>
>> but I have found a lot of peppers, where people have applied constant
>> surface tension simulation using Semi-isotropic coupling. Assuming that the
>> stretching of the membrane is produced via difference in the ref_p along z
>> and xy directions, does the pcoupltype=surface-tension mandatory for such
>> simulations ? Should the xy compressibility be switched to zero assuming
>> that I am interesting in the modeling of stretching of the membrane?
>>
>> 2017-09-25 17:15 GMT+02:00 André Farias de Moura <mo...@ufscar.br>:
>>
>>> it is quite well explained in the manual, pcoupltype=surface-tension
>>> Andre
>>>
>>> On Mon, Sep 25, 2017 at 5:38 AM, Own 12121325 <own12121...@gmail.com>
>>> wrote:
>>>
>>> > Dear Gromacs users!
>>> >
>>> > I wonder to ask whether is possible to perform simulations in NPgT
>>> ensemble
>>> > with the explicit definition of the surface tension value. My system is
>>> > composed of the lipid bilayer solvated in water.
>>> >
>>> > I have found that switching compressibility along x-y to zero and
>>> > introducing bigger negative ref_p along this direction will produce
>>> lateral
>>> > tension on the bilayer according to
>>> >
>>> > g =b*(Pz – Py), where b - is the averaged height of the simulation box
>>> >
>>> >
>>> > I wonder to ask if it also can be realized instead via introduction of
>>> some
>>> > gamma_tension constant as a scaling factor ?
>>> >
>>> >
>>> > Thanks you!
>>> >
>>> >
>>> > Gleb
>>> > --
>>> > Gromacs Users mailing list
>>> >
>>> > * Please search the archive at http://www.gromacs.org/
>>> > Support/Mailing_Lists/GMX-Users_List before posting!
>>> >
>>> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>> >
>>> > * For (un)subscribe requests visit
>>> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>>> > send a mail to gmx-users-requ...@gromacs.org.
>>>
>>>
>>>
>>>
>>> --
>>> _
>>>
>>> Prof. Dr. André Farias de Moura
>>> Department of Chemistry
>>> Federal University of São Carlos
>>> São Carlos - Brazil
>>> phone: +55-16-3351-8090
>>> --
>>> Gromacs Users mailing list
>>>
>>> * Please search the archive at http://www.gromacs.org/Support
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>>
>>
>>
>
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Re: [gmx-users] Simulation in NPgT ensemble

[Own 12121325]

So the question - what the difference will be between A and B and what
method is better for the lipid bilayer?

(A)
pcoupltype = semiisotropic
tau_p 1 1
compressibility 4.5e-5 4.5e-5
ref_p -100 1

if the system size in the z-direction is ~ 10nm, then
this should give a surface tension of (Pz-Plat)*Lz ==
(1+100)bar*10 nm ~ 10^3 bar nm = 10^3*10^5 N/m2 *10^-9
m
=100mN/m assuming the z-dimension Lz remains
approximately 10 nm throughout the window of
calculation.


(B)
pcoupltype = surface-tension
tau_p 1 1
compressibility 4.5e-5 0 ; Z is fixed
ref_p -1000 1 ; -1000 is actual surface tension which is the compression
for the membrane along xy.

2017-09-25 17:29 GMT+02:00 Own 12121325 <own12121...@gmail.com>:

> Thanks, Andre!
>
> but I have found a lot of peppers, where people have applied constant
> surface tension simulation using Semi-isotropic coupling. Assuming that the
> stretching of the membrane is produced via difference in the ref_p along z
> and xy directions, does the pcoupltype=surface-tension mandatory for such
> simulations ? Should the xy compressibility be switched to zero assuming
> that I am interesting in the modeling of stretching of the membrane?
>
> 2017-09-25 17:15 GMT+02:00 André Farias de Moura <mo...@ufscar.br>:
>
>> it is quite well explained in the manual, pcoupltype=surface-tension
>> Andre
>>
>> On Mon, Sep 25, 2017 at 5:38 AM, Own 12121325 <own12121...@gmail.com>
>> wrote:
>>
>> > Dear Gromacs users!
>> >
>> > I wonder to ask whether is possible to perform simulations in NPgT
>> ensemble
>> > with the explicit definition of the surface tension value. My system is
>> > composed of the lipid bilayer solvated in water.
>> >
>> > I have found that switching compressibility along x-y to zero and
>> > introducing bigger negative ref_p along this direction will produce
>> lateral
>> > tension on the bilayer according to
>> >
>> > g =b*(Pz – Py), where b - is the averaged height of the simulation box
>> >
>> >
>> > I wonder to ask if it also can be realized instead via introduction of
>> some
>> > gamma_tension constant as a scaling factor ?
>> >
>> >
>> > Thanks you!
>> >
>> >
>> > Gleb
>> > --
>> > Gromacs Users mailing list
>> >
>> > * Please search the archive at http://www.gromacs.org/
>> > Support/Mailing_Lists/GMX-Users_List before posting!
>> >
>> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>> >
>> > * For (un)subscribe requests visit
>> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>> > send a mail to gmx-users-requ...@gromacs.org.
>>
>>
>>
>>
>> --
>> _
>>
>> Prof. Dr. André Farias de Moura
>> Department of Chemistry
>> Federal University of São Carlos
>> São Carlos - Brazil
>> phone: +55-16-3351-8090
>> --
>> Gromacs Users mailing list
>>
>> * Please search the archive at http://www.gromacs.org/Support
>> /Mailing_Lists/GMX-Users_List before posting!
>>
>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>
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>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>> send a mail to gmx-users-requ...@gromacs.org.
>
>
>
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Re: [gmx-users] Simulation in NPgT ensemble

[Own 12121325]

Thanks, Andre!

but I have found a lot of peppers, where people have applied constant
surface tension simulation using Semi-isotropic coupling. Assuming that the
stretching of the membrane is produced via difference in the ref_p along z
and xy directions, does the pcoupltype=surface-tension mandatory for such
simulations ? Should the xy compressibility be switched to zero assuming
that I am interesting in the modeling of stretching of the membrane?

2017-09-25 17:15 GMT+02:00 André Farias de Moura <mo...@ufscar.br>:

> it is quite well explained in the manual, pcoupltype=surface-tension
> Andre
>
> On Mon, Sep 25, 2017 at 5:38 AM, Own 12121325 <own12121...@gmail.com>
> wrote:
>
> > Dear Gromacs users!
> >
> > I wonder to ask whether is possible to perform simulations in NPgT
> ensemble
> > with the explicit definition of the surface tension value. My system is
> > composed of the lipid bilayer solvated in water.
> >
> > I have found that switching compressibility along x-y to zero and
> > introducing bigger negative ref_p along this direction will produce
> lateral
> > tension on the bilayer according to
> >
> > g =b*(Pz – Py), where b - is the averaged height of the simulation box
> >
> >
> > I wonder to ask if it also can be realized instead via introduction of
> some
> > gamma_tension constant as a scaling factor ?
> >
> >
> > Thanks you!
> >
> >
> > Gleb
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at http://www.gromacs.org/
> > Support/Mailing_Lists/GMX-Users_List before posting!
> >
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
> > * For (un)subscribe requests visit
> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > send a mail to gmx-users-requ...@gromacs.org.
>
>
>
>
> --
> _
>
> Prof. Dr. André Farias de Moura
> Department of Chemistry
> Federal University of São Carlos
> São Carlos - Brazil
> phone: +55-16-3351-8090
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/
> Support/Mailing_Lists/GMX-Users_List before posting!
>
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[gmx-users] Simulation in NPgT ensemble

[Own 12121325]

Dear Gromacs users!

I wonder to ask whether is possible to perform simulations in NPgT ensemble
with the explicit definition of the surface tension value. My system is
composed of the lipid bilayer solvated in water.

I have found that switching compressibility along x-y to zero and
introducing bigger negative ref_p along this direction will produce lateral
tension on the bilayer according to

g =b*(Pz – Py), where b - is the averaged height of the simulation box


I wonder to ask if it also can be realized instead via introduction of some
gamma_tension constant as a scaling factor ?


Thanks you!


Gleb
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[gmx-users] NPT or NPgT ensemble simulation for shear deformations

[Own 12121325]

Dear Gromacs users!

I wonder to ask regarding mdp setups for the simulation of membrane
bilayers with the introduction of DEFORM (non-equilibrium MD) with the aim
to simulate a shearing of the water.

1 -  assuming that I'm doing a simulation using semi-isotropic coupling,
does the switching of the xy compressibility to zero automatically means
switching to NPgT (constant surface tension) ensemble without any further
modifications in mdp file?

2 - which of the ensemble should produce more realistic behaviour of the
system with the application of the DEFORM along c(x) or c(y) directions?

Thank you!
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[gmx-users] Set up the deformation rates for DEFORM

[Own 12121325]

Hello,

with the aim to simulate a shear stress using DEFORM non-equilibrium
option, I need to calibrate the deformations rates of the box (nm ps-1)
against the experimental value characterized for shear stress (10 dyn/cm2 ~
1 pascal).

Therefore, I would like to know what deformations rates set up in mdp file
should correspond to the value of the 10 dyn/cm2, assuming that I am
simulating my system with standard params for the barostat? I would be
grateful for some formula suitable for such reasonable conversions.

Thanks!

Gleb
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[gmx-users] Set up the deformation rates for DEFORM

[Own 12121325]

Hello,

with the aim to simulate a shear stress using DEFORM non-equilibrium
option, I need to calibrate the deformations rates of the box (nm ps-1)
against the experimental value characterized for shear stress (10 dyn/cm2 ~
1 pascal).

Therefore, I would like to know what deformations rates set up in mdp file
should correspond to the value of the 10 dyn/cm2, assuming that I am
simulating my system with standard params for the barostat? I would be
grateful for some formula suitable for such reasonable conversions.

Thanks!

Gleb
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[gmx-users] On the setting tau_t for SD integrator for membrane protein simulation

[Own 12121325]

Dear Gromacs users!

I would like to use Langevin's thermostat in my simulation of the membrane
protein. I am interesting what values of tau_t will be appropriate for such
simulation, assuming that I would like to create a "soft" equilibration
conditions with slower relaxation times via coupling of the system to the
medium with higher viscosity.

Thanks!

Micky
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[gmx-users] Modeling of the shear flow of the liquid using DEFORM

[Own 12121325]

Dear GROMACS users,

I would like to perform non-equilibrium simulation adding a shear flow on
the liquid in my bio-membrane system composed of lipids and water. By means
of the applications of the deformations I would like to shear a water in
X-Y dimensions along the surface of the membrane. Assuming that I make
modeling of the system in NPT ensemble with anisotropic coupling, will the
following options be correct for the setup?

compressibility = 0 0 4.5e-5 0.0 0.0 0.0 # here I sen compressibility for
all of the deformed directions xx, yy, xy etc to zero
ref_p   = 1.0135 1.0135 1.0135 0.0 0.0 0.0
; Deformation is on
Deform = 0 0 0 0.01 0.01 0.01 # here I add vel. 0.01 nm ps to the
non-diagonal elements corresponded to x and y dimensions of the box to
shear a liquid along it

Thanks so much for help!

Micky
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